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(v1.5.0.9016) only_rsi_columns update, documentation

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dr. M.S. (Matthijs) Berends
2021-02-08 14:18:42 +01:00
parent 8fda473e49
commit 4a84894f79
88 changed files with 654 additions and 375 deletions
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2
man/ab_property.Rd
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@ -72,7 +72,7 @@ ab_property(x, property = "name", language = get_locale(), ...)
Use these functions to return a specific property of an antibiotic from the \link{antibiotics} data set. All input values will be evaluated internally with \code{\link[=as.ab]{as.ab()}}.
}
\details{
All output will be \link{translate}d where possible.
All output \link[=translate]{will be translated} where possible.
The function \code{\link[=ab_url]{ab_url()}} will return the direct URL to the official WHO website. A warning will be returned if the required ATC code is not available.
}

33
man/antibiotic_class_selectors.Rd
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@ -14,42 +14,45 @@
\alias{fluoroquinolones}
\alias{glycopeptides}
\alias{macrolides}
\alias{oxazolidinones}
\alias{penicillins}
\alias{tetracyclines}
\title{Antibiotic Class Selectors}
\usage{
ab_class(ab_class, only_rsi_columns = NULL)
ab_class(ab_class, only_rsi_columns = FALSE)
aminoglycosides(only_rsi_columns = NULL)
aminoglycosides(only_rsi_columns = FALSE)
carbapenems(only_rsi_columns = NULL)
carbapenems(only_rsi_columns = FALSE)
cephalosporins(only_rsi_columns = NULL)
cephalosporins(only_rsi_columns = FALSE)
cephalosporins_1st(only_rsi_columns = NULL)
cephalosporins_1st(only_rsi_columns = FALSE)
cephalosporins_2nd(only_rsi_columns = NULL)
cephalosporins_2nd(only_rsi_columns = FALSE)
cephalosporins_3rd(only_rsi_columns = NULL)
cephalosporins_3rd(only_rsi_columns = FALSE)
cephalosporins_4th(only_rsi_columns = NULL)
cephalosporins_4th(only_rsi_columns = FALSE)
cephalosporins_5th(only_rsi_columns = NULL)
cephalosporins_5th(only_rsi_columns = FALSE)
fluoroquinolones(only_rsi_columns = NULL)
fluoroquinolones(only_rsi_columns = FALSE)
glycopeptides(only_rsi_columns = NULL)
glycopeptides(only_rsi_columns = FALSE)
macrolides(only_rsi_columns = NULL)
macrolides(only_rsi_columns = FALSE)
penicillins(only_rsi_columns = NULL)
oxazolidinones(only_rsi_columns = FALSE)
tetracyclines(only_rsi_columns = NULL)
penicillins(only_rsi_columns = FALSE)
tetracyclines(only_rsi_columns = FALSE)
}
\arguments{
\item{ab_class}{an antimicrobial class, like \code{"carbapenems"}. The columns \code{group}, \code{atc_group1} and \code{atc_group2} of the \link{antibiotics} data set will be searched (case-insensitive) for this value.}
\item{only_rsi_columns}{a logical to indicate whether only columns of class \href{[rsi]}{\verb{<rsi>}} must be selected. If set to \code{NULL} (default), it will be \code{TRUE} if any column of the data was \href{[rsi]}{transformed to class \verb{<rsi>}} on beforehand, and \code{FALSE} otherwise.}
\item{only_rsi_columns}{a logical to indicate whether only columns of class \href{[rsi]}{\verb{<rsi>}} must be selected (defaults to \code{FALSE})}
}
\description{
These functions help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. \strong{\Sexpr{ifelse(as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2, paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}

4
man/eucast_rules.Rd
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@ -26,7 +26,7 @@ eucast_rules(
version_breakpoints = 11,
version_expertrules = 3.2,
ampc_cephalosporin_resistance = NA,
only_rsi_columns = any(is.rsi(x)),
only_rsi_columns = FALSE,
...
)
@ -49,7 +49,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 11)
\item{ampc_cephalosporin_resistance}{a character value that should be applied for AmpC de-repressed cephalosporin-resistant mutants, defaults to \code{NA}. Currently only works when \code{version_expertrules} is \code{3.2}; '\emph{EUCAST Expert Rules v3.2 on Enterobacterales}' states that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these agents. A value of \code{NA} for this argument will remove results for these agents, while e.g. a value of \code{"R"} will make the results for these agents resistant. Use \code{NULL} to not alter the results for AmpC de-repressed cephalosporin-resistant mutants. \cr For \emph{EUCAST Expert Rules} v3.2, this rule applies to: \emph{Citrobacter braakii}, \emph{Citrobacter freundii}, \emph{Citrobacter gillenii}, \emph{Citrobacter murliniae}, \emph{Citrobacter rodenticum}, \emph{Citrobacter sedlakii}, \emph{Citrobacter werkmanii}, \emph{Citrobacter youngae}, \emph{Enterobacter}, \emph{Hafnia alvei}, \emph{Klebsiella aerogenes}, \emph{Morganella morganii}, \emph{Providencia} and \emph{Serratia}.}
\item{only_rsi_columns}{a logical to indicate whether only antibiotic columns must be detected that were \href{[rsi]}{transformed to class \verb{<rsi>}} on beforehand. Defaults to \code{TRUE} if any column of \code{x} is of class \verb{<rsi>}.}
\item{only_rsi_columns}{a logical to indicate whether only antibiotic columns must be detected that were \href{[rsi]}{transformed to class \verb{<rsi>}} on beforehand (defaults to \code{FALSE})}
\item{...}{column name of an antibiotic, see section \emph{Antibiotics} below}

117
man/filter_ab_class.Rd
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@ -13,6 +13,7 @@
\alias{filter_fluoroquinolones}
\alias{filter_glycopeptides}
\alias{filter_macrolides}
\alias{filter_oxazolidinones}
\alias{filter_penicillins}
\alias{filter_tetracyclines}
\title{Filter Isolates on Result in Antimicrobial Class}
@ -22,35 +23,121 @@ filter_ab_class(
ab_class,
result = NULL,
scope = "any",
only_rsi_columns = any(is.rsi(x)),
only_rsi_columns = FALSE,
...
)
filter_aminoglycosides(x, result = NULL, scope = "any", ...)
filter_aminoglycosides(
x,
result = NULL,
scope = "any",
only_rsi_columns = FALSE,
...
)
filter_carbapenems(x, result = NULL, scope = "any", ...)
filter_carbapenems(
x,
result = NULL,
scope = "any",
only_rsi_columns = FALSE,
...
)
filter_cephalosporins(x, result = NULL, scope = "any", ...)
filter_cephalosporins(
x,
result = NULL,
scope = "any",
only_rsi_columns = FALSE,
...
)
filter_1st_cephalosporins(x, result = NULL, scope = "any", ...)
filter_1st_cephalosporins(
x,
result = NULL,
scope = "any",
only_rsi_columns = FALSE,
...
)
filter_2nd_cephalosporins(x, result = NULL, scope = "any", ...)
filter_2nd_cephalosporins(
x,
result = NULL,
scope = "any",
only_rsi_columns = FALSE,
...
)
filter_3rd_cephalosporins(x, result = NULL, scope = "any", ...)
filter_3rd_cephalosporins(
x,
result = NULL,
scope = "any",
only_rsi_columns = FALSE,
...
)
filter_4th_cephalosporins(x, result = NULL, scope = "any", ...)
filter_4th_cephalosporins(
x,
result = NULL,
scope = "any",
only_rsi_columns = FALSE,
...
)
filter_5th_cephalosporins(x, result = NULL, scope = "any", ...)
filter_5th_cephalosporins(
x,
result = NULL,
scope = "any",
only_rsi_columns = FALSE,
...
)
filter_fluoroquinolones(x, result = NULL, scope = "any", ...)
filter_fluoroquinolones(
x,
result = NULL,
scope = "any",
only_rsi_columns = FALSE,
...
)
filter_glycopeptides(x, result = NULL, scope = "any", ...)
filter_glycopeptides(
x,
result = NULL,
scope = "any",
only_rsi_columns = FALSE,
...
)
filter_macrolides(x, result = NULL, scope = "any", ...)
filter_macrolides(
x,
result = NULL,
scope = "any",
only_rsi_columns = FALSE,
...
)
filter_penicillins(x, result = NULL, scope = "any", ...)
filter_oxazolidinones(
x,
result = NULL,
scope = "any",
only_rsi_columns = FALSE,
...
)
filter_tetracyclines(x, result = NULL, scope = "any", ...)
filter_penicillins(
x,
result = NULL,
scope = "any",
only_rsi_columns = FALSE,
...
)
filter_tetracyclines(
x,
result = NULL,
scope = "any",
only_rsi_columns = FALSE,
...
)
}
\arguments{
\item{x}{a data set}
@ -61,7 +148,7 @@ filter_tetracyclines(x, result = NULL, scope = "any", ...)
\item{scope}{the scope to check which variables to check, can be \code{"any"} (default) or \code{"all"}}
\item{only_rsi_columns}{a logical to indicate whether only columns must be included that were \href{[rsi]}{transformed to class \verb{<rsi>}} on beforehand. Defaults to \code{TRUE} if any column of \code{x} is of class \verb{<rsi>}.}
\item{only_rsi_columns}{a logical to indicate whether only columns must be included that were \href{[rsi]}{transformed to class \verb{<rsi>}} on beforehand (defaults to \code{FALSE})}
\item{...}{arguments passed on to \code{\link[=filter_ab_class]{filter_ab_class()}}}
}

16
man/first_isolate.Rd
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@ -12,7 +12,7 @@ Methodology of this function is strictly based on:
}
\usage{
first_isolate(
x,
x = NULL,
col_date = NULL,
col_patient_id = NULL,
col_mo = NULL,
@ -33,7 +33,7 @@ first_isolate(
)
filter_first_isolate(
x,
x = NULL,
col_date = NULL,
col_patient_id = NULL,
col_mo = NULL,
@ -41,7 +41,7 @@ filter_first_isolate(
)
filter_first_weighted_isolate(
x,
x = NULL,
col_date = NULL,
col_patient_id = NULL,
col_mo = NULL,
@ -50,7 +50,7 @@ filter_first_weighted_isolate(
)
}
\arguments{
\item{x}{a \link{data.frame} containing isolates. Can be left blank for automatic determination.}
\item{x}{a \link{data.frame} containing isolates. Can be left blank for automatic determination, see \emph{Examples}.}
\item{col_date}{column name of the result date (or date that is was received on the lab), defaults to the first column with a date class}
@ -130,7 +130,7 @@ There are two ways to determine whether isolates can be included as first weight
Any difference from S to R (or vice versa) will (re)select an isolate as a first weighted isolate. With \code{ignore_I = FALSE}, also differences from I to S|R (or vice versa) will lead to this. This is a reliable method and 30-35 times faster than method 2. Read more about this in the \code{\link[=key_antibiotics]{key_antibiotics()}} function.
\item Using \code{type = "points"} and argument \code{points_threshold}
A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds \code{points_threshold}, which default to \code{2}, an isolate will be (re)selected as a first weighted isolate.
A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds \code{points_threshold}, which defaults to \code{2}, an isolate will be (re)selected as a first weighted isolate.
}
}
@ -151,10 +151,12 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
# `example_isolates` is a data set available in the AMR package.
# See ?example_isolates.
# basic filtering on first isolates
example_isolates[first_isolate(), ]
example_isolates[first_isolate(example_isolates), ]
\donttest{
# faster way, only works in R 3.2 and later:
example_isolates[first_isolate(), ]
# get all first Gram-negatives
example_isolates[which(first_isolate() & mo_is_gram_negative()), ]

4
man/guess_ab_col.Rd
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@ -8,7 +8,7 @@ guess_ab_col(
x = NULL,
search_string = NULL,
verbose = FALSE,
only_rsi_columns = any(is.rsi(x))
only_rsi_columns = FALSE
)
}
\arguments{
@ -18,7 +18,7 @@ guess_ab_col(
\item{verbose}{a logical to indicate whether additional info should be printed}
\item{only_rsi_columns}{a logical to indicate whether only antibiotic columns must be detected that were \href{[rsi]}{transformed to class \verb{<rsi>}} on beforehand. Defaults to \code{TRUE} if any column of \code{x} is of class \verb{<rsi>}.}
\item{only_rsi_columns}{a logical to indicate whether only antibiotic columns must be detected that were \href{[rsi]}{transformed to class \verb{<rsi>}} on beforehand (defaults to \code{FALSE})}
}
\value{
A column name of \code{x}, or \code{NULL} when no result is found.

4
man/key_antibiotics.Rd
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@ -6,7 +6,7 @@
\title{Key Antibiotics for First (Weighted) Isolates}
\usage{
key_antibiotics(
x,
x = NULL,
col_mo = NULL,
universal_1 = guess_ab_col(x, "amoxicillin"),
universal_2 = guess_ab_col(x, "amoxicillin/clavulanic acid"),
@ -125,7 +125,7 @@ There are two ways to determine whether isolates can be included as first weight
Any difference from S to R (or vice versa) will (re)select an isolate as a first weighted isolate. With \code{ignore_I = FALSE}, also differences from I to S|R (or vice versa) will lead to this. This is a reliable method and 30-35 times faster than method 2. Read more about this in the \code{\link[=key_antibiotics]{key_antibiotics()}} function.
\item Using \code{type = "points"} and argument \code{points_threshold}
A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds \code{points_threshold}, which default to \code{2}, an isolate will be (re)selected as a first weighted isolate.
A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds \code{points_threshold}, which defaults to \code{2}, an isolate will be (re)selected as a first weighted isolate.
}
}

21
man/mdro.Rd
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@ -20,33 +20,28 @@ See the supported guidelines above for the list of publications used for this fu
}
\usage{
mdro(
x,
x = NULL,
guideline = "CMI2012",
col_mo = NULL,
info = interactive(),
pct_required_classes = 0.5,
combine_SI = TRUE,
verbose = FALSE,
only_rsi_columns = any(is.rsi(x)),
only_rsi_columns = FALSE,
...
)
custom_mdro_guideline(..., as_factor = TRUE)
brmo(x, guideline = "BRMO", only_rsi_columns = any(is.rsi(x)), ...)
brmo(x = NULL, only_rsi_columns = FALSE, ...)
mrgn(x, guideline = "MRGN", only_rsi_columns = any(is.rsi(x)), ...)
mrgn(x = NULL, only_rsi_columns = FALSE, ...)
mdr_tb(x, guideline = "TB", only_rsi_columns = any(is.rsi(x)), ...)
mdr_tb(x = NULL, only_rsi_columns = FALSE, ...)
mdr_cmi2012(x, guideline = "CMI2012", only_rsi_columns = any(is.rsi(x)), ...)
mdr_cmi2012(x = NULL, only_rsi_columns = FALSE, ...)
eucast_exceptional_phenotypes(
x,
guideline = "EUCAST",
only_rsi_columns = any(is.rsi(x)),
...
)
eucast_exceptional_phenotypes(x = NULL, only_rsi_columns = FALSE, ...)
}
\arguments{
\item{x}{a \link{data.frame} with antibiotics columns, like \code{AMX} or \code{amox}. Can be left blank for automatic determination.}
@ -63,7 +58,7 @@ eucast_exceptional_phenotypes(
\item{verbose}{a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.}
\item{only_rsi_columns}{a logical to indicate whether only antibiotic columns must be detected that were \href{[rsi]}{transformed to class \verb{<rsi>}} on beforehand. Defaults to \code{TRUE} if any column of \code{x} is of class \verb{<rsi>}.}
\item{only_rsi_columns}{a logical to indicate whether only antibiotic columns must be detected that were \href{[rsi]}{transformed to class \verb{<rsi>}} on beforehand (defaults to \code{FALSE})}
\item{...}{in case of \code{\link[=custom_mdro_guideline]{custom_mdro_guideline()}}: a set of rules, see section \emph{Using Custom Guidelines} below. Otherwise: column name of an antibiotic, see section \emph{Antibiotics} below.}

6
man/mo_property.Rd
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@ -126,11 +126,11 @@ Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and so
The Gram stain - \code{\link[=mo_gramstain]{mo_gramstain()}} - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, \href{https://pubmed.ncbi.nlm.nih.gov/11837318}{PMID 11837318}), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive - all other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value \code{NA}. Functions \code{\link[=mo_is_gram_negative]{mo_is_gram_negative()}} and \code{\link[=mo_is_gram_positive]{mo_is_gram_positive()}} always return \code{TRUE} or \code{FALSE} (except when the input is \code{NA} or the MO code is \code{UNKNOWN}), thus always return \code{FALSE} for species outside the taxonomic kingdom of Bacteria.
Determination of yeasts - \code{\link[=mo_is_yeast]{mo_is_yeast()}} - will be based on the taxonomic phylum, class and order. Budding yeasts are true fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). The true yeasts are separated into one main order Saccharomycetales. For all microorganisms that are in one of those two groups, the function will return \code{TRUE}. It returns \code{FALSE} for all other taxonomic entries.
Determination of yeasts - \code{\link[=mo_is_yeast]{mo_is_yeast()}} - will be based on the taxonomic kingdom and class. \emph{Budding yeasts} are fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). \emph{True yeasts} are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are fungi and member of the taxonomic class Saccharomycetes, the function will return \code{TRUE}. It returns \code{FALSE} otherwise (except when the input is \code{NA} or the MO code is \code{UNKNOWN}).
Intrinsic resistance - \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} - will be determined based on the \link{intrinsic_resistant} data set, which is based on \href{https://www.eucast.org/expert_rules_and_intrinsic_resistance/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2} (2020). The \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} can be vectorised over arguments \code{x} (input for microorganisms) and over \code{ab} (input for antibiotics).
Intrinsic resistance - \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} - will be determined based on the \link{intrinsic_resistant} data set, which is based on \href{https://www.eucast.org/expert_rules_and_intrinsic_resistance/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2} (2020). The \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} functions can be vectorised over arguments \code{x} (input for microorganisms) and over \code{ab} (input for antibiotics).
All output will be \link{translate}d where possible.
All output \link[=translate]{will be translated} where possible.
The function \code{\link[=mo_url]{mo_url()}} will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.
}

2
man/resistance_predict.Rd
View File

@ -47,7 +47,7 @@ ggplot_rsi_predict(
)
}
\arguments{
\item{x}{a \link{data.frame} containing isolates. Can be left blank for automatic determination.}
\item{x}{a \link{data.frame} containing isolates. Can be left blank for automatic determination, see \emph{Examples}.}
\item{col_ab}{column name of \code{x} containing antimicrobial interpretations (\code{"R"}, \code{"I"} and \code{"S"})}